// Note: the training atoms are needed for patching up chain breaks
// when reading in conformations.
InFilePrefix /projects/kestrel/users/karplus/burial/undertaker/atoms-inputs/
ReadTrainingAtoms monomeric-50pc.atoms
ReadRotamerLibrary monomeric-50pc.rot

InFilePrefix /projects/kestrel/users/karplus/burial/undertaker/spots/
    ReadAtomType pdb-name.types
    ReadClashTable pdb-atom-name.clash
    SetClashDefinition pdb-atom-name

CreateBurialCost dry5 monomeric-50pc-dry-5.spot smoothed-monomeric-50pc-dry-5.hist

CreateBurialCost wet6.5 monomeric-50pc-wet-6.5.spot smoothed-monomeric-50pc-wet-6.5.hist log
CreateBurialCost dry6.5 monomeric-50pc-dry-6.5.spot smoothed-monomeric-50pc-dry-6.5.hist
CreateBurialCost gen6.5 monomeric-50pc-generic-6.5.spot smoothed-monomeric-50pc-generic-6.5.hist

CreateBurialCost dry8 monomeric-50pc-dry-8.spot smoothed-monomeric-50pc-dry-8.hist
CreateBurialCost dry10 monomeric-50pc-dry-10.spot smoothed-monomeric-50pc-dry-10.hist
CreateBurialCost dry12 monomeric-50pc-dry-12.spot smoothed-monomeric-50pc-dry-12.hist

CreateAlphaCost alpha monomeric-smoothed-alpha.hist
CreateAlphaCost alpha_prev  monomeric-smoothed-alpha-1.hist -1

Time


//Need to read in target before specific fragments or alignments can
// be read, also before constraints can be defined.

InFilePrefix 

ReadTargetPDB T0138.blank.pdb
NameTarget T0138
PopConform	// get rid of unneeded all-zero conformation


InFilePrefix /projects/compbio/lib/alphabet/
ReadAlphabet alpha.alphabet
InFilePrefix
CreatePredAlphaCost pred_alpha2 alpha11 T0138.t2k.alpha.rdb 2 alpha alpha_prev

// These disulphides don't look as promising as they once did--
// but we may want to add them back in. 
// SSbond 20 53
// C8-C34 looks better than C20-C53
SSbond 8 34

Constraint	595	771	2.3 2.7 3.2 // V77 N Y99  O
Constraint	600	783	2.3 2.7 3.2 // V77 O S101 N
Constraint	609	787 	2.3 2.7 3.2	// A79 N S101 O
Constraint	612	794 	2.3 2.7 3.2	// A79 O E103 N
Constraint	622	801 	2.3 2.7 3.2	// V81 N E103 O
Constraint	627	811 	2.3 2.7 3.2	// V81 O H105 N
Constraint	636	819 	2.3 2.7 3.2	// G83 N H105 O

//Add CB constraints
Constraint	597	775	3 5.12 7	// CBs V77	H100
Constraint	604	785	3 5.12 7	// CBs P78	S101
Constraint	611	791	3 5.12 7	// CBs A79	A102
Constraint	616	796	3 5.12 7	// CBs I80	E103
Constraint	624	805	3 5.12 7	// CBs V81	L104
Constraint	632	813	3 5.12 7	// CBs V82	H105


// Hbonds from try4-opt for middle strand.
// Constraint	422	620	2.0 2.7 3.2	// L54 N I80 O
// Constraint	428	629	2.0 2.7 3.2	// L54 O V82 N
// Constraint	53	406 2.0 2.7 3.2	// C8  N I51 O
// Constraint	57	416 2.0 2.7 3.2	// C8  O C53 N
// Constraint	67	420 2.0 2.7 3.2	// W10 N C53 O

// trying to slide the middle strand back 2 to match 2ry predictions 
 Constraint	438	620	2.0 2.7 3.2	// L56 N I80 O
 Constraint	444	629	2.0 2.7 3.2	// L56 O V82 N
 Constraint	53	420 	2.0 2.7 3.2	// C8  N C53 O
 Constraint	57	430 	2.0 2.7 3.2	// C8  O I55 N
 Constraint	67	436	2.0 2.7 3.2	// W10 N I55 O
Constraint	79	446	2.0 2.7 3.2	// W10 O V57 N


// trying to make strand 3 stay straight
 Constraint	784	795	7  7.3  8	// CAs S101 G103
 Constraint	754	822	22 29.15 35	// CAs L98 L106

// trying to make helices stay straight
Constraint	284	356	10 13.5 16	// CAs G37 T46
Constraint	485	558	10 13.5 16	// CAs F63 F72

SetCost gen6.5 0.2 wet6.5 0.2 dry5 3 dry6.5 5 dry8 3 dry12 2 \
	phobic_fit 1 \
	sidechain 0.2 \
	clashes 4 sidechain_clashes -0.2 backbone_clashes 1.5 \
	break 12  \
	constraints 0.15 \
	pred_alpha2 2 \
	contact_order 0.7 \
	known_ssbond 0.005


//	radius_norm 0 radius_fit 0.2 \